BOL: Related items

GOLD:Genomes Online Database

Jit — Wed, 26 Jul 2017 07:49:29 -0500

GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

coursera genome assembly tutorial

Jit — Sat, 25 Nov 2017 08:57:25 -0600

Solutions to Coursera Genome Sequencing (Bioinformatics II)

Address of the bookmark: https://github.com/iansealy/coursera-assembly

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

Jit — Wed, 06 Dec 2017 02:08:14 -0600

An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/cope

Mash: fast genome and metagenome distance estimation using MinHash

Jit — Tue, 12 Dec 2017 17:30:12 -0600

Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is available in and GCC >= 4.8 and OSX >= 10.7.

See http://mash.readthedocs.org for more information.

Address of the bookmark: https://github.com/marbl/Mash/releases

GIGGLE: a search engine for large-scale integrated genome analysis

Jit — Wed, 10 Jan 2018 03:10:45 -0600

GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.

https://www.nature.com/articles/nmeth.4556

Address of the bookmark: https://github.com/ryanlayer/giggle

MUMmer4: A fast and versatile genome alignment system

Jit — Sat, 03 Feb 2018 04:59:17 -0600

MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query sequences. With a theoretical limit on the input size of 141Tbp, MUMmer4 can now work with input sequences of any biologically realistic length. We show that as a result of these enhancements, the nucmer program in MUMmer4 is easily able to handle alignments of large genomes;

Address of the bookmark: https://mummer4.github.io/

G-compass: a comparative genome browser

Jit — Thu, 12 Apr 2018 10:00:27 -0500

G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their ortholog information were derived from H-InvDB and its subdatabase Evola, respectively. G-compass is available for free of charge. [ Sample ]

Address of the bookmark: http://www.h-invitational.jp/g-compass/

EAGLER: a scaffolding tool for long reads.

Jit — Mon, 04 Jun 2018 05:26:03 -0500

EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

Mac OS X 10.11.1
Mac OS X 10.10.3
Ubuntu 14.04 LTS

https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER

Download blasr 1.3 version

Jit — Fri, 15 Jun 2018 03:01:20 -0500

DOWNLOAD LINK: https://github.com/BioInf-Wuerzburg/proovread/raw/master/util/blasr-1.3.1/blasr

I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error:

fail to open file './temporarySam'

[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 161.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70989574 sequences have been processed.
[main] Version: 0.7.15-r1140
[main] CMD: bwa aln -t 30 all_p_ctg.fa -
[main] Real time: 2402.523 sec; CPU: 53429.488 sec
[E::hts_open_format] Failed to open file temporarySam
samtools sort: can't open "temporarySam": No such file or directory
[bwa_aln_core] convert to sequence coordinate... 1.00 sec
[bwa_aln_core] refine gapped alignments... 6.07 sec
[bwa_aln_core] print alignments... PREPROCESS:
Fastq format is recognized
[Thu Jun 14 18:16:47 2018] Building bwa index...
bwa index -p all_p_ctg.fa /home/urbe/Tools/OPERA-LG_v2.0.6/all_p_ctg.fa
[Thu Jun 14 18:18:35 2018] Finding the SA coordinates of the reads using BWA aln...
[Thu Jun 14 18:58:37 2018] Generate alignments of reads using bwa sampe...
bwa samse -n 1 all_p_ctg.fa read.sai - | grep '\(^@\|XT:A:U\)' | /usr/local/bin/samtools view -S -h -b -F 0x4 - | /usr/local/bin/samtools sort -@ 20 -no - temporarySam > FALCON-Unzip-Scaff.bam
Mapping long-reads using blasr...
/home/urbe/Tools/SSpace/SSPACE-LongRead_v1-1/blasr -nproc 40 -m 1 -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates 1 -maxAnchorsPerPosition 1 -sdpTupleSize 7 /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta /home/urbe/Tools/OPERA-LG_v2.0.6/all_p_ctg.fa | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > FALCON-Unzip-Scaff.map
sh: 1: /home/urbe/Tools/SSpace/SSPACE-LongRead_v1-1/blasr: Permission denied
Sorting mapping results...
sort -k1,1 -k9,9g FALCON-Unzip-Scaff.map > FALCON-Unzip-Scaff.map.sort
Analyzing sorted results...
Extracting linking information...
i3 2000 5000
i2 1000 2000
i4 5000 15000
i0 -200 300
i5 15000 40000
i1 300 1000
Repeat detection...
/home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2
Illegal division by zero at /home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl line 93.
readline() on closed filehandle FILE at bin/OPERA-long-read.pl line 250.
rm anchor_contig_info.dat contig_length.dat filtered_edges.dat filtered_edges_cov.dat *.sai
rm: cannot remove 'anchor_contig_info.dat': No such file or directory
mv FALCON-Unzip-Scaff.bam FALCON-Unzip-Scaff-with-repeat.bam
/home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_repeat.pl FALCON-Unzip-Scaff-with-repeat.bam repeat.dat | /usr/local/bin/samtools view - -h -S -b > FALCON-Unzip-Scaff.bam
rm FALCON-Unzip-Scaff-with-repeat.bam
/home/urbe/Tools/OPERA-LG_v2.0.6/bin/OPERA-LG config > log
Analyzing 1 library: FALCON-Unzip-Scaff.bam
min library mean : 0
minimum contig length is 500
Current library: 1 out of 7
Analyzing file: pairedEdges_no_repeat_i0
Analyzing file: pairedEdges_no_repeat_i1
Analyzing file: pairedEdges_no_repeat_i2
Analyzing file: pairedEdges_no_repeat_i3
Analyzing file: pairedEdges_no_repeat_i4
Analyzing file: pairedEdges_no_repeat_i5
ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta

To resolve this, try downloading blasr version 1.3 above and re-run :)

Nanopolis: polish a genome assembly

Rahul Nayak — Thu, 26 Jul 2018 04:51:28 -0500

Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

Quickstart

http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

Algorithms

http://simpsonlab.github.io/2017/06/30/nanopolish-v0.7.0/

Address of the bookmark: https://github.com/jts/nanopolish